Protesters who clashed with police have vowed to keep blockading a work site for Melbourne’s East West Link road project.

A few dozen protesters linked arms and blocked entrances to a drilling site in Fitzroy on Tuesday in a bid to stop work.

But police moved in and began removing the protesters, pulling several of them off a fence around the site.

One of the protest leaders, Anthony Main, says police were heavy-handed in dealing with them with people being thrown to the ground.

He urged protesters to keep linking arms at the site, preventing workers from entering, after police surrounded the fence.

"This protest is going to be the death of this government," he said.

A line of protesters now stands beside a line of police around the site but no scuffles have broken out since the early morning clash.

Acting Assistant Commissioner Rick Nugent said it was disappointing to see the protest turn ugly and police felt they were caught in the middle of the dispute.

He said he wasn't aware of accusations of police brutality but police had an obligation to help workers gain access to the site. Work has now been called off for the day because of the protest.

"We fully support people to protest peacefully. We would like to work with the protesters for that to occur, but where people clearly break the law then we're obliged to take some action," he told reporters at the scene.

"It is illegal to blockade roads, footpaths and prevent the work from occurring. And it's illegal to assault police and resist arrest."

One person has been arrested for assaulting police. Another has climbed over a fence and is standing on a drill rig, but police say they have no plans to forcibly remove her.

Protesters have repeatedly targeted drill rigs and followed workers from site to site in a bid to stop the completion of preliminary work on the multi-billion-dollar road project, which will link the city's Eastern Freeway and CityLink.